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HIBAG

HIBAG

A tool for imputation of human leukocyte antigen (HLA) types using single nucleotide polymorphisms (SNPs). The HIBAG algorithm consolidates attribute bagging and an ensemble classifier methods, with haplotype inference for SNPs and HLA types.

Topic

Immunoproteins, genes and antigens; Immunology; DNA polymorphism; Population genetics

Details

  • Operation: Imputation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 1.20.0
  • Maturity: Stable
  • Credit: The National Institutes of Health (NIH), Medical Research Council, United Kingdom
  • Contact: zhengx _at_ u.washington.edu
  • Collection: BioConductor

Publications

Zheng X, Shen J, Cox C, Wakefield JC, Ehm MG, Nelson MR, Weir BS "HIBAG--HLA genotype imputation with attribute bagging." Pharmacogenomics J. 2014 Apr;14(2):192-200. May 28. https://doi.org/10.1038/tpj.2013.18
PMID: 23712092
PMCID: PMC3772955

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Ole AK, Pags H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600

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